2. Methods

There are two steps to performing BBM, which are implemented in the BayesBrainMap R package: (1) prior estimation and (2) model fitting (Figure 1).

Figure 1: Overview of Bayesian Brain Mapping.

Global Signal Regression Group ICA Parcellation
15 HCP ICs 25 HCP ICs 50 HCP ICs Yeo 17
With GSR ✔ ✔ ✔ ✔
Without GSR ✔ ✔ ✔ ✔

Templates used for Bayesian brain mapping.

2.3 Workflow Overview

Setup

To reproduce this workflow, first follow the setup process outlined in Appendix A.

3. Choosing Training Subjects

  1. Filter Subjects by Sufficient fMRI Scan Duration

    See Appendix B.1 and script: 1_fd_time_filtering.R

  2. Filter Unrelated Subjects

    See Appendix B.2 and script: 2_unrelated_filtering.R

  3. Balance sex within age groups

    See Appendix B.3 and script: 3_balance_age_sex.R

The resulting subject list (valid_combined_subjects_balanced.rds) is used throughout the rest of the analysis.

4. Step 1: Estimate Priors using estimate_prior()

In this step, we estimate group-level statistical priors using the estimate_prior() function from the BayesBrainMap package.

4.1 Subject List and Scan Selection

The encoding parameter is set to combined, LR, and RL to use the final lists of subjects saved in Step 3.3 (valid_combined_subjects_balanced.rds, valid__LR_subjects_balanced.rds, and valid_RL_subjects_balanced.rds). The combined list includes individuals who passed motion filtering in both LR and RL directions for both sessions, were unrelated, and were sex-balanced within age groups. The LR and RL lists include subjects who met these criteria independently for each direction.

If encoding is combined, we include only REST1 sessions from both phase-encoding directions:

If encoding is LR or RL, we use both REST1 and REST2 sessions from the specified direction:

For LR:

For RL:

4.2 Temporal Preprocessing Parameters

To standardize scan duration and improve data quality, we apply both initial volume dropping and temporal truncation using parameters handled directly by the estimate_prior() function from the BayesBrainMap package.

Specifically:

See Appendix C for more details.

4.3 Parcellation Choices

We consider three types of group-level parcellations for estimating priors:

Each of these parcellations was used to estimate priors with and without global signal regression (GSR), resulting in eight total priors saved as .rds files. See Table 1 [TODO link] for a summary of the parcellations and GSR combinations.

# This script estimates and saves functional connectivity priors 
# for both spatial topography and connectivity.
# It supports both GICA-based (15/25/50 ICs) and Yeo17 parcellations, 
# with or without global signal regression (GSR).
# For priors using the "combined" subject list, it loads REST1-LR and REST1-RL
# scans for each subject, 
# drops the first 15 volumes, and truncates each scan to approximately 10 minutes.
# Outputs:
# - Priors `.rds` file saved in `dir_results`

source("5_estimate_prior.R")

4.4 Example Usage

Running estimate_prior() on the full "combined" subject list (~350 subjects) takes approximately 27 hours and uses 135 GB of memory.

For an example of how to run estimate_prior() and all relevant parameters, see Appendix E.

5. Visualization

In this section, we visualize both the parcellation maps and the priors outputs (mean and variance) for each parcellation scheme used in the study: Yeo17, 15 IC, 25 IC, and 50 IC using the combined list of subjects.

We also visualize their corresponding functional connectivity (FC) priors.

5.1 Generate and Save Parcellation Visualizations

5.1.1 Yeo17 parcellation

Script: 8_visualization_Yeo17parcellations.R

This script creates one PNG image per parcel (17 in total), where only the selected parcel is colored and all others are white. The parcellation used is Yeo17, created in Appendix D.

Images are saved in data-OSF/outputs/parcellations_plots/Yeo17.

5.1.2 GICA Parcellations

Script: 9_visualization_GICAparcellations.R

This script loops over all independent components for each parcellation dimensionality (nIC = 15, 25, 50) and generates two images per component:

  • A cortical surface map (e.g., GICA15_IC1.png)

  • A subcortical view (e.g., GICA15_IC1_sub.png)

The resulting images are saved in the following folders:

  • data_OSF/outputs/parcellations_plots/GICA15/

  • data_OSF/outputs/parcellations_plots/GICA25

  • data_OSF/outputs/parcellations_plots/GICA50

Each pair of files corresponds to a specific ICA component and captures its spatial map across brain regions.

5.2 Visualize Prior Components

Script: 6_visualization_prior.R

This script loads each estimated prior file from priors_rds/ and plots both the mean and standard deviation components for all independent components (ICs).

All images are organized into folders by number of ICs, GSR setting, and corresponding list of subjects used, e.g.:

data_OSF/priors_plots/GICA15/combined/GSR/

data_OSF/priors_plots/GICA15/combined/noGSR/

data_OSF/priors_plots/GICA25/LR/noGSR/

data_OSF/priors_plots/Yeo17/RL/GSR/
...

5.3 Visual Summary of Priors

In this section, we present a comparative visual summary of the estimated group-level priors.

For each parcellation type Yeo17, 15 ICs, 25 ICs, and 50 IC, we display:

  • First and Last Parcellation Map

  • First and Last Component Mean

  • First and Last Component Standard Deviation

These summaries are shown in a 2-column grid layout per parcellation to highlight spatial structure and variability.

All images were generated using the scripts:

  • 8_visualization_Yeo17parcellations.R

  • 9_visualization_GICAparcellations.R

  • 6_visualization_prior.R

5.3.1 15 ICs

IC Component Mean Standard Deviation
IC1
IC15

5.3.2 25 ICs

IC Component Mean Standard Deviation
IC1
IC25

5.3.3 50 ICs

IC Component Mean Standard Deviation
IC1
IC50

5.3.4 Yeo17

Network Component Mean Standard Deviation
DefaultA
DorsAttnA

5.3.5 Mix

TODO: For the paper instead of here?

Network Component Mean Standard Deviation
Yeo17 DefaultA
GICA15 IC 2
GICA25 IC 2
GICA50 IC 12
MSC Default
PROFUMO 1

5.4 Visualize Functional Connectivity Priors

Script: 7_visualization_FC.R

This step visualizes the Functional Connectivity (FC) prior for each prior using both the Cholesky and Inverse-Wishart parameterizations. For each group-level prior in priors/, we compute and plot:

  • Mean FC matrix (off-diagonal values only)

  • Standard deviation of FC estimates (from the variance matrix)

For each prior, the following outputs are saved in the corresponding folder under:

data_OSF/outputs/priors_plots/<parcellation>/<encoding>/FC/

Where:

  • parcellation = GICA15, GICA25, GICA50, or Yeo17

  • encoding = LR, RL, or combined

PDF files (2 per prior)

  • [prior_name]_FC_Cholesky.pdf

  • [prior_name]_FC_InverseWishart.pdf

Each PDF includes:

  • FC Prior Mean (Page 1)

  • FC Prior Standard Deviation (Page 2)

PNG imgaes (4 per prior)

  • [prior_name]_FC_Cholesky_mean.png

  • [prior_name]_FC_Cholesky_sd.png

  • [prior_name]_FC_InverseWishart_mean.png

  • [prior_name]_FC_InverseWishart_sd.png

These visualizations allow for a direct comparison of spatial FC structure and uncertainty across priors and estimation methods.

The figures below show the mean and standard deviation of FC priors for each parcellation (GICA15, GICA25, GICA50, Yeo17) using Cholesky and Inverse-Wishart methods. Only combined priors are shown.

5.4.1 GICA15

5.4.2 25 ICs

5.4.3 50 ICs

5.4.4 Yeo17

6. Step 2: Using Priors for Individual-Level Brain Mapping

In this section, we demonstrate how to apply the population-level priors estimated in Section 4 to perform subject-level analysis using the BayesBrainMap package.

The process involves two steps:

  1. Fitting the Bayesian brain mapping model to subject data using a precomputed prior.

  2. Identifying regions of significant deviation from the prior mean (i.e., areas of engagement).

This example uses:

6.1 Load Subject-Level fMRI Data and Prior

# Load population prior 
prior <- readRDS("priors/Yeo17/prior_combined_Yeo17_GSR.rds")

# Load subject fMRI data (CIFTI format)
BOLD <- c(file.path(dir_data, "inputs", 
                    "rfMRI_REST1_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii"),
          file.path(dir_data, "inputs", 
                    "rfMRI_REST1_RL_Atlas_MSMAll_hp2000_clean.dtseries.nii"))

The fMRI input must be a CIFTI, NIFTI, or matrix object compatible with the prior.

6.2 Estimate Subject-Level Networks

Once the data is loaded, we fit the Bayesian brain mapping model to obtain individualized functional networks aligned to the prior components:

bMap <- BrainMap(
  BOLD = BOLD,
  prior = prior,
  TR = 0.72,
  drop_first = 15
  )

6.3 Identify Engagement Maps

eng <- engagements(
  bMap = bMap
  )

6.4 Visualize the Results

We now plot:

  1. The subject-level networks estimated by BrainMap() (both mean and standard error).

  2. The engagement maps, showing regions of deviation from the prior mean.

For all outputs, we only visualize ContA network from the Yeo 17 parcellation.

Appendix A: Setup

To reproduce this workflow, first clone the repository to your local machine or cluster:

git clone https://github.com/mandymejia/BayesianBrainMapping-Templates.git
cd BayesianBrainMapping-Templates

Next, download the required data_OSF/ and priors folders from the following OSF link:

https://osf.io/n3wk5/?view_only=0d95b31090a245eb9ef51fe262be60ef

Once downloaded, unzip the folder and place in the folder in the GitHub directory with the same corresponding name. The folder structure should look like this:

BayesianBrainMapping-Templates/
├── data_OSF/
│   ├── inputs/
│   └── outputs/
├── priors/
│   ├── GICA15/
│   └── ...
├── src/
│   ├── 0_setup.R
│   └── 1_fd_time_filtering.R
|   └── ...
├── BayesianBrainMapping-Templates.Rmd
└── ...

This section initializes the environment by loading required packages, setting analysis parameters, and defining directory paths.

Important: Before running the workflow, you must review 0_setup.R and install any necessary packages, ensure you have an installation of Connectome Workbench, and update the following variables to match your local or cluster environment:

github_repo_dir <- getwd()
src_dir <- file.path(github_repo_dir, "src")
source(file.path(src_dir, "0_setup.R"))

Appendix B: Subject Filtering

Appendix B.1: Filter Subjects by Sufficient fMRI Scan Duration

We begin by filtering subjects based on the fMRI scan duration after motion scrubbing For each subject, and for each session (REST1, REST2) and encoding direction (LR, RL), we compute framewise displacement (FD) using the fMRIscrub package. We use a lagged and filtered version of FD (Phạm et al. 2023) (Power et al. 2012) (Fair et al. 2009) appropriate for multiband data. FD is calculated from the Movement_Regressors.txt file available in the HCP data for each subject, encoding and session.

A volume is considered valid if it passes an FD threshold, and a subject is retained only if both sessions in both encodings have at least 10 minutes (600 seconds) of valid data.

The final subject lists include those who passed the filtering criteria separately for each encoding: LR, RL, and their intersection, referred to as thecombined list. The combined list includes only subjects who passed all criteria for both LR and RL encodings across both visits (REST1 and REST2), and is the one used throughout this project.

# This script filters subjects based on motion using framewise displacement (FD)
# from fMRIscrub.
# For each subject, encoding (LR/RL), and session (REST1/REST2), it computes FD,
# flags volumes exceeding the FD threshold of 0.5 mm (scrubbing), 
# and calculates valid scan time after excluding those high-motion volumes.
# Subjects with ≥10 minutes of valid data in both sessions are retained.
# Outputs (saved in dir_results):
# - Valid subject lists for LR, RL, and combined encodings (intersection)
# - FD summary per subject/session/encoding

#set up path, etc.
github_repo_dir <- getwd()
src_dir <- file.path(github_repo_dir, "src")
source(file.path(src_dir, "0_setup.R"))

#run script to exclude sessions based on head motion
source(file.path(src_dir,"1_fd_time_filtering.R"))

During this step, an FD summary table is generated with the following columns:

  • subject: HCP subject ID

  • session: REST1 or REST2

  • encoding: LR or RL

  • mean_fd: mean framewise displacement

  • valid_time_sec: total duration of valid data in seconds

Preview of FD Summary Table

X subject session encoding mean_fd valid_time_sec
1 100206 REST1 LR 0.1017240 858.24
2 100206 REST2 LR 0.1361220 858.96
3 100206 REST1 RL 0.0698779 864.00
4 100206 REST2 RL 0.0824894 863.28

As shown above, subject 100206 qualifies for further analysis because each of the four sessions (REST1/REST2 × LR/RL) contains at least 600 seconds of valid data.

The script is currently designed to filter based on valid time only, but it can be easily adapted to apply additional constraints such as maximum mean FD thresholds if desired (e.g., mean_fd < 0.1).

Appendix B.2: Filter Unrelated Subjects

Building on the previous step, we use the HCP restricted demographic data to exclude related individuals. This step helps ensure the statistical independence of subjects in the group-level priors estimation.

For the LR, RL, and combined lists of valid subjects derived in the previous step, we:

  1. Subset the HCP restricted demographics to include only those subjects with at least 10 minutes remaining after scrubbing.

  2. Filter by Family_ID to retain a single individual per family.

Note: This step requires access to the HCP restricted data. If you do not have access, you can skip this step, resulting in some related subjects being included in your training data.

# This script filters subjects to retain only unrelated individuals, using Family ID 
# information from the restricted HCP data.
# For each encoding (LR, RL, combined), it selects one subject per family from the 
# FD-valid lists.
# Outputs (saved in dir_personal due to restricted data):
# - Unrelated subject lists for LR, RL, and combined encodings (intersection)

source(file.path(src_dir,"2_unrelated_filtering.R"))

Appendix B.3: Balance Sex Within Age Groups

In the final step of subject selection, we balance sex across age groups to reduce potential demographic bias in priors estimation.

For the LR, RL, and combined lists of valid subjects derived in the previous step, we:

  • Subset the HCP unrestricted demographics to include only those subjects.

  • Split subjects by age group and examine the sex distribution within each group.

  • If both sexes are present but imbalanced, we randomly remove subjects from the overrepresented group to achieve balance.

Note: If the unrelated subject filtering step is skipped (e.g., due to lack of restricted data access), the code automatically falls back to using valid_<encoding>_subjects_FD instead of valid_<encoding>_subjects_unrelated.

The final list of valid subjects is saved in dir_results as:

  • valid_<encoding>_subjects_balanced.csv

  • valid_<encoding>_subjects_balanced.rds (used in the prior estimation step)

# This script balances sex within each age group for subjects who passed FD and 
# unrelated filtering.
# For each encoding (LR, RL, combined), it samples subjects to equalize the number
# of males and females per age group, 
# unless an age group includes only one gender (in which case no balancing is applied).
# Uses age and gender information from the unrestricted HCP data.
# Outputs (saved in dir_personal):
# - Sex-balanced subject lists for LR, RL, and combined encodings (as .csv and .rds)

source(file.path(src_dir,"3_balance_age_sex.R"))

Appendix C: Scrubbing and Temporal Truncation

Given the HCP TR of 0.72 seconds, 10 minutes corresponds to:

T_total <- floor(600 / TR_HCP) # ~833 volumes

To define the volumes to scrub (i.e., exclude beyond 10 minutes), we compute:

T_scrub_start <- T_total + 1
scrub_BOLD1 <- replicate(length(BOLD_paths1), T_scrub_start:nT_HCP, simplify = FALSE)
scrub_BOLD2 <- replicate(length(BOLD_paths2), T_scrub_start:nT_HCP, simplify = FALSE)
scrub <- list(scrub_BOLD1, scrub_BOLD2)

Because drop_first = 15 removes frames before truncation, the final retained time series per scan will be slightly shorter than 10 minutes. Approximately:

(833 - 15) * 0.72 = ~589 seconds (~9.8 minutes)

Appendix D: Prepare Yeo17 Parcellation for Prior Estimation

In this step, we load and preprocess a group-level cortical parcellation to be used as the template to estimate the priors in the next step. Specifically, we use the Yeo 17-network parcellation (Yeo_17) and perform the following operations:

The resulting parcellation is saved as Yeo17_simplified_mwall.rds.

# This script simplifies the Yeo 17-network parcellation by collapsing region 
# labels and masking out the medial wall.
# It creates a cleaned version of the parcellation suitable for downstream analyses.
# Output:
# - Saved as RDS file in dir_data: "Yeo17_simplified_mwall.rds"

source(file.path(src_dir,"4_parcellations.R"))

We can visualize the Yeo17 networks and their corresponding labels:

# Load libraries
library(ciftiTools)
library(rgl)
rgl::setupKnitr()

# Load the parcellation
yeo17 <- readRDS(file.path(dir_data, "outputs", "Yeo17_simplified_mwall.rds"))
yeo17 <- add_surf(yeo17)

view_xifti_surface(
  xifti = yeo17,
  widget = TRUE,
  title = "Yeo17 Network Parcellation",
  legend_ncol = 6,
  legend_fname = file.path(dir_data, "outputs", "parcellations_plots", 
                           "Yeo17", "Yeo17_legend.png"),
  fname=file.path(dir_data, "outputs", "parcellations_plots", "Yeo17")
)

Appendix E: Example Function Call for Prior Estimation

# For detailed parameter descriptions, run: ?estimate_prior

estimate_prior(
  BOLD = BOLD_paths1,         # REST1 LR scans (list of file paths)
  BOLD2 = BOLD_paths2,        # REST2 LR scans (same subjects/order as BOLD)
  template = GICA,            # GICA 15-component parcellation (CIFTI dscalar file path)
  GSR = TRUE,                 # Apply global signal regression
  TR = 0.72,                  # Repetition time in seconds
  hpf = 0.01,                 # High-pass filter cutoff in Hz
  Q2 = 0,                     # No nuisance IC denoising
  drop_first = 15,            # Drop first 15 volumes
  scrub = scrub,              # Timepoints to scrub (list format)
  verbose = TRUE              # Print progress updates
)

References

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Gordon, Evan M, Timothy O Laumann, Adrian W Gilmore, Dillan J Newbold, Deanna J Greene, Jeffrey J Berg, Mario Ortega, et al. 2017. “Precision Functional Mapping of Individual Human Brains.” Neuron 95 (4): 791–807.
Phạm, Damon, Daniel J McDonald, Lei Ding, Mary Beth Nebel, and Amanda F Mejia. 2023. “Less Is More: Balancing Noise Reduction and Data Retention in fMRI with Data-Driven Scrubbing.” NeuroImage 270: 119972.
Power, Jonathan D, Kelly A Barnes, Abraham Z Snyder, Bradley L Schlaggar, and Steven E Petersen. 2012. “Spurious but Systematic Correlations in Functional Connectivity MRI Networks Arise from Subject Motion.” Neuroimage 59 (3): 2142–54.
Yeo, BT Thomas, Fenna M Krienen, Jorge Sepulcre, Mert R Sabuncu, Danial Lashkari, Marisa Hollinshead, Joshua L Roffman, et al. 2011. “The Organization of the Human Cerebral Cortex Estimated by Intrinsic Functional Connectivity.” Journal of Neurophysiology.